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Merge pull request #218 from PolinaBevad/fix_issue_204_mapq_insertion
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Fixed issue 204: wrong calculations of MAPQ
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@pcingola
pcingola authored May 21, 2019
2 parents bba8266 + 00b510b commit f70d926
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Showing 24 changed files with 451 additions and 450 deletions.
9 changes: 5 additions & 4 deletions src/main/java/com/astrazeneca/vardict/modules/VariationRealigner.java
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Expand Up @@ -2448,13 +2448,14 @@ void adjRefFactor(Variation ref, double factor_f) {
if (instance().conf.y) {
System.err.printf(" AdjRefFactor: %s %s\n", ref.varsCount, factor_f);
}

int oldVarsCount = ref.varsCount;
ref.varsCount -= (int) (factor_f * ref.varsCount);
ref.highQualityReadsCount -= (int) (factor_f * ref.highQualityReadsCount);
ref.lowQualityReadsCount -= (int) (factor_f * ref.lowQualityReadsCount);
ref.meanPosition -= factor_f * ref.meanPosition;
ref.meanQuality -= factor_f * ref.meanQuality;
ref.meanMappingQuality -= factor_f * ref.meanMappingQuality;
double factorCnt = oldVarsCount != 0 ? Math.abs((ref.varsCount - oldVarsCount)) / (double) oldVarsCount : 1;
ref.meanPosition -= ref.meanPosition * factor_f * factorCnt;
ref.meanQuality -= ref.meanQuality * factor_f * factorCnt;
ref.meanMappingQuality -= ref.meanMappingQuality * factor_f * factorCnt;
ref.numberOfMismatches -= factor_f * ref.numberOfMismatches;
ref.varsCountOnForward -= (int) (factor_f * ref.varsCountOnForward);
ref.varsCountOnReverse -= (int) (factor_f * ref.varsCountOnReverse);
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6 changes: 3 additions & 3 deletions ...mplicon;hg19.fa;Colo829-18_S3-sort.bam;chr1;933866-934466;933866-934466;-a 100.95 -D;.txt
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@@ -1,6 +1,6 @@
Amplicon,hg19.fa,Colo829-18_S3-sort.bam,chr1,933866,934466,933866,934466,-a 10:0.95 -D
Colo829-18_S3-sort testbed chr1 934099 934099 G C 4 4 0 0 2 2 C/C 1.0000 0;2 50.0 1 32.8 1 60.0 3.000 1.0000 0 0 3.000 1 4.0 3 3 CAACGCGGGGGCAGAGGGCG GTGCGCATGCGGGGCTGCAG chr1:933867-934466 SNV 1 1 0 0 C:4:F-2:R-2:1.0000:2:50.0:1:32.8:1:1.0000:60.0:3.000 Good0 4 4 0 0 2 2 C/C 1.0000 0;2 50.0 1 32.8 1 60.0 3.000 1.0000 0 chr1:933867-934466
Colo829-18_S3-sort testbed chr1 934106 934106 A G 4 3 1 0 1 2 A/G 0.7500 0;2 53.3 1 36.3 1 60.0 6.000 0.7500 0 0 1.000 1 4.7 3 4 GGGGCAGAGGGCGGGTGCGC TGCGGGGCTGCAGGGATGCG chr1:933867-934466 SNV 1 1 0 0 A:1:F-1:R-0:0.2500:0:40.0:0:41.0:0:0.2500:60.0:2.000 & G:3:F-1:R-2:0.7500:2:53.3:1:36.3:1:0.7500:60.0:6.000 Good0 4 3 1 0 1 2 A/G 0.7500 0;2 53.3 1 36.3 1 60.0 6.000 0.7500 0 chr1:933867-934466
Colo829-18_S3-sort testbed chr1 934123 934123 T TGCGGAGGGGAGGGCGCGGA 8 2 2 2 1 1 T/+19 0.2500 2;2 38.7 1 37.8 1 70.4 4.000 0.6667 0.2500 27 2.000 5 1.2 2 3 CGCATGCGGGGCTGCAGGGA GCGGAGGGGAGGGCGCGGAG chr1:933867-934466 Insertion 1 1 0 0 T:4:F-2:R-2:0.5000:2:35.5:0:15.1:1:0.3333:49.6:0.333 & I+GCGGAGGGGAGGGCGCGGA:2:F-1:R-1:0.2500:2:38.7:1:37.8:1:0.6667:70.4:4.000 Good0 8 2 2 2 1 1 T/+19 0.2500 2;2 38.7 1 37.8 1 70.4 4.000 0.6667 0.2500 chr1:933867-934466
Colo829-18_S3-sort testbed chr1 934144 934144 C G 8 6 0 0 2 4 G/G 0.7500 0;2 17.0 1 36.7 1 60.0 12.000 0.6000 0 0 2.000 1 3.0 6 10 GCGGAGGGGAGGGCGCGGAG GGAGGGCGCGGAGCGGAGGG chr1:933867-934466 SNV 1 1 0 0 G:6:F-2:R-4:0.7500:2:17.0:1:36.7:1:0.6000:60.0:12.000 & I+GGAGG:2:F-1:R-1:0.2500:2:22.7:0:32.5:1:0.1000:62.0:1.000 & I+GGAGGGCGCGGAGCGGAGGGGAGGGCGCGGAGCGGAGG:3:F-1:R-2:0.3750:2:40.0:1:39.9:1:0.3000:68.0:6.000 Good0 8 6 0 0 2 4 G/G 0.7500 0;2 17.0 1 36.7 1 60.0 12.000 0.6000 0 chr1:933867-934466 Good1 8 3 0 0 1 2 G/+38 0.3750 0;2 40.0 1 39.9 1 68.0 6.000 0.3000 0.3750 chr1:933867-934466
Colo829-18_S3-sort testbed chr1 934144 934144 C CGGAGGGCGCGGAGCGGAGGGGAGGGCGCGGAGCGGAGG 8 3 0 0 1 2 G/+38 0.3750 0;2 40.0 1 39.9 1 68.0 6.000 0.3000 0.3750 21 4.000 1 4.9 3 10 GCGGAGGGGAGGGCGCGGAG GGAGGGCGCGGAGCGGAGGG chr1:933867-934466 Insertion 1 1 0 0 G:6:F-2:R-4:0.7500:2:17.0:1:36.7:1:0.6000:60.0:12.000 & I+GGAGG:2:F-1:R-1:0.2500:2:22.7:0:32.5:1:0.1000:62.0:1.000 & I+GGAGGGCGCGGAGCGGAGGGGAGGGCGCGGAGCGGAGG:3:F-1:R-2:0.3750:2:40.0:1:39.9:1:0.3000:68.0:6.000 Good0 8 6 0 0 2 4 G/G 0.7500 0;2 17.0 1 36.7 1 60.0 12.000 0.6000 0 chr1:933867-934466 Good1 8 3 0 0 1 2 G/+38 0.3750 0;2 40.0 1 39.9 1 68.0 6.000 0.3000 0.3750 chr1:933867-934466
Colo829-18_S3-sort testbed chr1 934123 934123 T TGCGGAGGGGAGGGCGCGGA 8 2 2 2 1 1 T/+19 0.2500 2;2 33.0 1 32.2 1 60.0 4.000 0.6667 0.2500 27 2.000 5 1.2 2 3 CGCATGCGGGGCTGCAGGGA GCGGAGGGGAGGGCGCGGAG chr1:933867-934466 Insertion 1 1 0 0 T:4:F-2:R-2:0.5000:2:43.0:0:18.2:1:0.3333:60.0:0.333 & I+GCGGAGGGGAGGGCGCGGA:2:F-1:R-1:0.2500:2:33.0:1:32.2:1:0.6667:60.0:4.000 Good0 8 2 2 2 1 1 T/+19 0.2500 2;2 33.0 1 32.2 1 60.0 4.000 0.6667 0.2500 chr1:933867-934466
Colo829-18_S3-sort testbed chr1 934144 934144 C G 8 6 0 0 2 4 G/G 0.7500 0;2 17.0 1 36.7 1 60.0 12.000 0.6000 0 0 2.000 1 3.0 6 10 GCGGAGGGGAGGGCGCGGAG GGAGGGCGCGGAGCGGAGGG chr1:933867-934466 SNV 1 1 0 0 G:6:F-2:R-4:0.7500:2:17.0:1:36.7:1:0.6000:60.0:12.000 & I+GGAGG:2:F-1:R-1:0.2500:2:22.0:0:31.5:1:0.1000:60.0:1.000 & I+GGAGGGCGCGGAGCGGAGGGGAGGGCGCGGAGCGGAGG:3:F-1:R-2:0.3750:2:35.3:1:35.2:1:0.3000:60.0:6.000 Good0 8 6 0 0 2 4 G/G 0.7500 0;2 17.0 1 36.7 1 60.0 12.000 0.6000 0 chr1:933867-934466 Good1 8 3 0 0 1 2 G/+38 0.3750 0;2 35.3 1 35.2 1 60.0 6.000 0.3000 0.3750 chr1:933867-934466
Colo829-18_S3-sort testbed chr1 934144 934144 C CGGAGGGCGCGGAGCGGAGGGGAGGGCGCGGAGCGGAGG 8 3 0 0 1 2 G/+38 0.3750 0;2 35.3 1 35.2 1 60.0 6.000 0.3000 0.3750 21 4.000 1 4.9 3 10 GCGGAGGGGAGGGCGCGGAG GGAGGGCGCGGAGCGGAGGG chr1:933867-934466 Insertion 1 1 0 0 G:6:F-2:R-4:0.7500:2:17.0:1:36.7:1:0.6000:60.0:12.000 & I+GGAGG:2:F-1:R-1:0.2500:2:22.0:0:31.5:1:0.1000:60.0:1.000 & I+GGAGGGCGCGGAGCGGAGGGGAGGGCGCGGAGCGGAGG:3:F-1:R-2:0.3750:2:35.3:1:35.2:1:0.3000:60.0:6.000 Good0 8 6 0 0 2 4 G/G 0.7500 0;2 17.0 1 36.7 1 60.0 12.000 0.6000 0 chr1:933867-934466 Good1 8 3 0 0 1 2 G/+38 0.3750 0;2 35.3 1 35.2 1 60.0 6.000 0.3000 0.3750 chr1:933867-934466
4 changes: 2 additions & 2 deletions ...h37.fa;NA24385_Insertion_chr20_60464465_60470068.bam;chr20;60464465-60470068;-f 0.001.txt
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Expand Up @@ -15,6 +15,6 @@ NA24385_Insertion_chr20_60465664_60468868 testbed chr20 60467252 60467252 T C 15
NA24385_Insertion_chr20_60465664_60468868 testbed chr20 60468259 60468259 C G 8 8 0 0 7 1 G/G 1.0000 0;2 30.9 1 38.2 1 52.5 16.000 1.0000 0.1250 1 1.000 1 3.2 8 8 GTGGATAAATGAATGGGTGG TGAATAGAGGGATAGATGGA chr20:60465665-60468868 SNV 0 0
NA24385_Insertion_chr20_60465664_60468868 testbed chr20 60468306 60468307 GT AG 11 3 6 1 3 0 GT/AG 0.2727 2;0 17.0 0 41.0 0 58.0 6.000 0.3000 0 0 3.000 4 1.3 3 10 ACCACAGGGATGGTGGATGG GGGTGGGTGGATGGATAGAT chr20:60465665-60468868 Complex 0 0
NA24385_Insertion_chr20_60465664_60468868 testbed chr20 60467272 60467272 C T 14 14 0 0 3 11 T/T 1.0000 0;2 33.1 1 40.3 1 60.0 28.000 1.0000 0.0714 1 2.000 2 2.2 14 14 TAAAGCCCGTTGGTGACTCA AGCTGTCCACAGACTGTCCA chr20:60465665-60468868 SNV 0 0
NA24385_Insertion_chr20_60465664_60468868 testbed chr20 60468290 60468290 C CAGGGATGGTGGATGGGTGGGTGGGTGGATGGATAGATGGATAGATATGTGAATAGAGAGATGGTGGATGGAGGGGTGGGTGGATAGATGGATGGGTGGGTGAATAG 11 8 0 0 7 1 +106/+106 0.7273 0;2 51.0 1 37.7 1 48.3 16.000 1.0000 0.6364 41 2.000 2 2.4 8 8 GATAGATGGATGGGTGACCA AGGGATGGTGGATGGGTGGG chr20:60465665-60468868 Insertion 0 0
NA24385_Insertion_chr20_60465664_60468868 testbed chr20 60468848 60468848 G GTGGA 12 7 3 1 6 1 G/+4 0.5833 2;2 37.8 1 39.0 1 57.6 14.000 0.7000 0.0833 15 4.000 4 0.6 7 10 GATGGTGGATGGGTGGGTGA TGGATGGATGGATGGGTGAA chr20:60465665-60468868 Insertion 0 0
NA24385_Insertion_chr20_60465664_60468868 testbed chr20 60468290 60468290 C CAGGGATGGTGGATGGGTGGGTGGGTGGATGGATAGATGGATAGATATGTGAATAGAGAGATGGTGGATGGAGGGGTGGGTGGATAGATGGATGGGTGGGTGAATAG 11 8 0 0 7 1 +106/+106 0.7273 0;2 41.8 1 30.9 1 39.6 16.000 1.0000 0.6364 41 2.000 2 2.4 8 8 GATAGATGGATGGGTGACCA AGGGATGGTGGATGGGTGGG chr20:60465665-60468868 Insertion 0 0
NA24385_Insertion_chr20_60465664_60468868 testbed chr20 60468848 60468848 G GTGGA 12 7 3 1 6 1 G/+4 0.5833 2;2 34.6 1 35.7 1 52.7 14.000 0.7000 0.0833 15 4.000 4 0.6 7 10 GATGGTGGATGGGTGGGTGA TGGATGGATGGATGGGTGAA chr20:60465665-60468868 Insertion 0 0
NA24385_Insertion_chr20_60465664_60468868 testbed chr20 60465775 60465775 G A 19 19 0 0 12 7 A/A 1.0000 0;2 37.1 1 37.3 1 60.0 5.333 1.0000 0 0 2.000 2 1.8 16 16 AGGATATAGCACCCAAGTAA TGTAAGCTATTTCTGGTTTT chr20:60465665-60468868 SNV 0 0
10 changes: 5 additions & 5 deletions ...Simple;GRCh37.fa;NA24385_chr_19_58559581-58567861.bam;chr20;58559581;58567861;-f0.001.txt
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@@ -1,14 +1,14 @@
Simple,GRCh37.fa,NA24385_chr_19_58559581_58567861.bam,chr19,58559581,58567861,-f 0.001
NA24385_chr_19_58559581_58567861 testbed 19 58564449 58564449 T TCCTGAGTAGCTGGGATTACAGGCGCACACCACCCCGCCCAGCTAATTTTTGTATTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTGGTGTCTAACTCCTCACCTCATGATCCACCTTCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCACCGGCCACATGTGCCCTTGTATCTTAAAGGACAGAACGGAGGACACAGGGGCCGTATTGAGCAGAGGAAGGGCCTGGACTTGGCTCAGTCACTGGGGTCCTCCGTGCCCCTGGGGAGCACAGGGAGATGCCAAGGCCATCCACTCACTACAGGTGACCCATCTCCCTCGCCCTCCACAGGGTCCCGGGCCCGCTTGCCTCTGAAGCCGAGTATCTGGGACGAGCCTGAGGACCTTCTCGCAGGGCCCTCCTCAGACCTGCGGGCAGAAGGGACTGTGATCTCGAGCCCCAAGGGTCCAAGTGCTCAGAGAATCAGTCCCCGAAGGAGAAACAGGAACACTGACCAGAGCGGCCGCCACCAGCCATCCCTCAAGCACACCAAAGGTGGTACCCAAGAGGCTGTTGCAGGCATCTCGGTAGTGCCGCGTGGGCCCCGAGGTGGGCGGC 38 2 16 4 2 0 T/+614 0.0526 2;0 37.6 1 37.2 1 72.8 4.000 0.1053 0.0526 33 3.000 1 1.2 2 19 GCGATTCTCCTGCCTCACCC CCTGAGTAGCTGGGATTACA 19:58559582-58567861 Insertion 0 2-4-2
NA24385_chr_19_58559581_58567861 testbed 19 58564449 58564449 T TCCTGAGTAGCTGGGATTACAGGCGCACACCACCCCGCCCAGCTAATTTTTGTATTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTGGTGTCTAACTCCTCACCTCATGATCCACCTTCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCACCGGCCACATGTGCCCTTGTATCTTAAAGGACAGAACGGAGGACACAGGGGCCGTATTGAGCAGAGGAAGGGCCTGGACTTGGCTCAGTCACTGGGGTCCTCCGTGCCCCTGGGGAGCACAGGGAGATGCCAAGGCCATCCACTCACTACAGGTGACCCATCTCCCTCGCCCTCCACAGGGTCCCGGGCCCGCTTGCCTCTGAAGCCGAGTATCTGGGACGAGCCTGAGGACCTTCTCGCAGGGCCCTCCTCAGACCTGCGGGCAGAAGGGACTGTGATCTCGAGCCCCAAGGGTCCAAGTGCTCAGAGAATCAGTCCCCGAAGGAGAAACAGGAACACTGACCAGAGCGGCCGCCACCAGCCATCCCTCAAGCACACCAAAGGTGGTACCCAAGAGGCTGTTGCAGGCATCTCGGTAGTGCCGCGTGGGCCCCGAGGTGGGCGGC 38 2 16 4 2 0 T/+614 0.0526 2;0 31.0 1 30.7 1 60.0 4.000 0.1053 0.0526 33 3.000 1 1.2 2 19 GCGATTCTCCTGCCTCACCC CCTGAGTAGCTGGGATTACA 19:58559582-58567861 Insertion 0 2-4-2
NA24385_chr_19_58559581_58567861 testbed 19 58563424 58563424 G GGGGACGGGAGTTAGGAGCCCCAGCTTGTAACAGTGACCCGAGCTGTGGCACAGGTCCCCTGGCTCCATCTAATGCTCTGTTGTCACTGTCCTGAAATGATCAACGATCTTTGAACAAGGGGATTTGCATTTCCATTTTGTACAGGGGCCCCTCGAATTCTGTCTCAGGTCCTGTTAAGAGCTCTTTAGGAGTGGTTATTTATTTTTTGTATAAGCAGAGTCTTGCTGTGTTGCCCAGGCTGGTCCCAAACTCCTGGCCTCAAGCAATCCTCCAGCATCAGCATCCCAAAGCACGGGAACAACAGGCGCGACACCGCGCACTGCCCTGGGACAGAGCCTTTGGGGATGACGCCCGTTCCTTGGTTGTTCGGTGGTGGTGGGGAGGATGGCTCCTGAGGGGCAGCTGCCGAACAGTCCTGTGCTTGCCATTCTAGGCGTCTGAGCTGATTCTGGATGCAGTGGCAGCAGCCCCAGCACTCCCCGAGGAAAGTGAGTGGCTGGAGACTACCCAGCTCCAGCAGAGTCTGCACACCAGGGCGGAGGCCGAAGCGCCCCGCGCCCCTGGCTTGCTGGGTGAGTCTGGCTCCTGTGTGGATTAAGGGTTGGAAATGGAGTTTGGGACTTCAACCCAAAGCCACAGACTTTGTTAATGGGTTGAGTTGGGTGCTTCGGTGGTGAACTCCACACTTCCCCCAGAAAGCATGCACACCTCCTGTGAGGACTGAGATCTGGGGCCCCTAGAACCACCATGTACATCGTTCACCCTACGAGAAGGGCCTCAGCCTCCGCACCTGAACGGCAGCCAAGGCAGACAGTCTGAGAGTGTTGGAGCACGGGGTTACCCAGA 24 2 12 0 2 0 G/+846 0.0833 0;0 22.0 1 42.0 1 60.0 4.000 0.1667 0.0833 70 5.000 1 0 2 12 GCAAGGACAGTGCAGCCTTG GGGACGGGAGTTAGGAGCCC 19:58559582-58567861 Insertion 0 2-0-0
NA24385_chr_19_58559581_58567861 testbed 19 58565460 58565460 T TG 45 5 21 19 2 3 T/+1 0.1111 2;2 51.5 1 40.3 1 62.0 10.000 0.1389 0 6 7.000 1 0.6 5 36 GCCACCCGGCCCTGAGTCCC GGGGGGAGCTGATGGGCCCC 19:58559582-58567861 Insertion 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58565460 58565460 T TG 45 5 21 19 2 3 T/+1 0.1111 2;2 49.8 1 39.0 1 60.0 10.000 0.1389 0 6 7.000 1 0.6 5 36 GCCACCCGGCCCTGAGTCCC GGGGGGAGCTGATGGGCCCC 19:58559582-58567861 Insertion 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58565418 58565419 GA G 30 2 21 7 0 2 A/-1 0.0667 2;0 28.5 1 34.4 1 60.0 4.000 0.0741 0.0333 1 2.000 1 0 2 27 CACGGCCCACGGCCACATGT ATGGCCAGCCTCGGGCCTCG 19:58559582-58567861 Deletion 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58565243 58565243 G GC 29 2 16 11 2 0 G/+1 0.0690 2;0 65.1 0 43.4 0 62.0 4.000 0.0690 0 6 7.000 1 1.0 2 29 TGGAGCCACCGAGGAAGAAA CCCCCCGGAGCAAGGGCCCC 19:58559582-58567861 Insertion 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58565243 58565243 G GC 29 2 16 11 2 0 G/+1 0.0690 2;0 63.0 0 42.0 0 60.0 4.000 0.0690 0 6 7.000 1 1.0 2 29 TGGAGCCACCGAGGAAGAAA CCCCCCGGAGCAAGGGCCCC 19:58559582-58567861 Insertion 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58565233 58565233 G A 30 19 5 6 12 7 G/A 0.6333 2;2 37.0 1 36.6 1 60.0 8.500 0.6071 0.0667 1 1.000 1 2.2 17 28 ATCCACCTGCTGGAGCCACC AGGAAGAAAGCCCCCCGGAG 19:58559582-58567861 SNV 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58564204 58564204 A G 44 2 11 31 1 1 A/G 0.0455 2;2 41.5 1 39.5 1 60.0 4.000 0.0476 0 0 1.000 1 1.0 2 42 CACCCTACGAGAAGGGCCTC GCCTCCGCACCTGAACGGCA 19:58559582-58567861 SNV 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58566218 58566218 A AT 13 3 0 10 0 3 A/+1 0.2308 0;0 15.2 1 41.0 1 63.6 6.000 0.2308 0.0769 10 11.000 1 0.4 3 13 TTTGTTTGACTTACAGAAGG TTTTTTTTTTAGATAGATGC 19:58559582-58567861 Insertion 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58566218 58566218 A AT 13 3 0 10 0 3 A/+1 0.2308 0;0 14.3 1 38.7 1 60.0 6.000 0.2308 0.0769 10 11.000 1 0.4 3 13 TTTGTTTGACTTACAGAAGG TTTTTTTTTTAGATAGATGC 19:58559582-58567861 Insertion 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58564329 58564330 CT C 16 8 1 6 1 7 T/-1 0.5000 2;2 41.4 1 41.4 1 54.9 16.000 0.5714 0.0625 14 15.000 1 2.1 8 14 TCTGCTCCCAAAACATGTGC TTTTTTTTTTTTTTCGAGAC 19:58559582-58567861 Deletion 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58565921 58565921 G GT 32 3 12 17 1 2 G/+1 0.0938 2;2 31.9 1 35.0 1 62.4 2.000 0.0690 0 7 8.000 1 0 2 29 TAACAGATAAACAGGGTTTT TTTTTTTCCTTTTTTGGGTA 19:58559582-58567861 Insertion 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58565921 58565921 G GT 32 3 12 17 1 2 G/+1 0.0938 2;2 30.7 1 33.7 1 60.0 2.000 0.0690 0 7 8.000 1 0 2 29 TAACAGATAAACAGGGTTTT TTTTTTTCCTTTTTTGGGTA 19:58559582-58567861 Insertion 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58562829 58562829 A T 2 2 0 0 0 2 T/T 1.0000 0;0 18.0 0 42.0 0 60.0 4.000 1.0000 0 0 1.000 1 1.0 2 2 TTAACTCCCTTCCTGCCATC GCTCCCTCCCTCCCTCCCTC 19:58559582-58567861 SNV 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58565086 58565087 GA G 40 2 13 23 0 2 A/-1 0.0500 2;0 28.0 0 34.5 1 60.0 4.000 0.0714 0 0 3.000 1 1.5 2 28 TTCCAGTGTGCCGACTGTGG TGGTCTTCACCTGGGTCACC 19:58559582-58567861 Deletion 0 0
NA24385_chr_19_58559581_58567861 testbed 19 58565732 58565734 GTC G 29 2 16 10 1 1 T/-2 0.0690 2;2 36.0 1 42.0 0 60.0 4.000 0.0741 0 2 2.000 2 0.5 2 27 CTTTCAGAAGCCTTGTCCAG TCCCTGTTAGCACCTGACTC 19:58559582-58567861 Deletion 0 0
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